I don't know much about the particulars of E-commerce and MBAs in that specific area. Seems like it would come under the umbrella of an MBA in general and you would have a specialty in that area. I would go for the general MBA and if the area really takes off, you can always get your PHd with a focus on E-commerce. Bottom line, get as much education while you are in the education getting mode, i.e., while you still in the college lifestyle.